Error(s) in re-building vignettes:
  ...
--- re-building 'cap-recap.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
--- finished re-building 'cap-recap.Rnw'

--- re-building 'colext.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
unmarked
 --- call from context --- 
unmarkedMultFrame(y = yy, yearlySiteCovs = list(year = year), 
    numPrimary = T)
 --- call from argument --- 
if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
 --- R stacktrace ---
where 1: unmarkedMultFrame(y = yy, yearlySiteCovs = list(year = year), 
    numPrimary = T)
where 2: eval(expr, .GlobalEnv)
where 3: eval(expr, .GlobalEnv)
where 4: withVisible(eval(expr, .GlobalEnv))
where 5: doTryCatch(return(expr), name, parentenv, handler)
where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 7: tryCatchList(expr, classes, parentenv, handlers)
where 8: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 10: evalFunc(ce, options)
where 11: tryCatchList(expr, classes, parentenv, handlers)
where 12: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 13: driver$runcode(drobj, chunk, chunkopts)
where 14: utils::Sweave(...)
where 15: engine$weave(file, quiet = quiet, encoding = enc)
where 16: doTryCatch(return(expr), name, parentenv, handler)
where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 18: tryCatchList(expr, classes, parentenv, handlers)
where 19: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
}, error = function(e) {
    OK <<- FALSE
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 20: tools:::.buildOneVignette("colext.Rnw", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/unmarked.Rcheck/vign_test/unmarked", 
    TRUE, FALSE, "colext", "", "/tmp/Rtmp27piSI/file22f444a0fe2.rds")

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (y, siteCovs = NULL, obsCovs = NULL, numPrimary, yearlySiteCovs = NULL) 
{
    J <- ncol(y)
    umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J))
    umf <- as(umf, "unmarkedMultFrame")
    umf@numPrimary <- numPrimary
    if (class(yearlySiteCovs) == "list") {
        yearlySiteVars <- names(yearlySiteCovs)
        for (i in seq(length(yearlySiteVars))) {
            if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", 
                "data.frame"))) 
                stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
            if (ncol(yearlySiteCovs[[i]]) != numPrimary | nrow(yearlySiteCovs[[i]]) != 
                nrow(y)) 
                stop("At least one matrix in yearlySiteCovs has incorrect number of dimensions.")
        }
        yearlySiteCovs <- data.frame(lapply(yearlySiteCovs, function(x) as.vector(t(x))))
    }
    umf@yearlySiteCovs <- yearlySiteCovs
    umf
}
<bytecode: 0xf3b3cb0>
<environment: namespace:unmarked>
 --- function search by body ---
Function unmarkedMultFrame in namespace unmarked has this body.
 ----------- END OF FAILURE REPORT -------------- 

Error: processing vignette 'colext.Rnw' failed with diagnostics:
 chunk 7 
Error in if (!(class(yearlySiteCovs[[i]]) %in% c("matrix", "data.frame"))) stop("At least one element of yearlySiteCovs is not a matrix or data frame.") : 
  the condition has length > 1

--- failed re-building 'colext.Rnw'

--- re-building 'distsamp.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
--- finished re-building 'distsamp.Rnw'

--- re-building 'spp-dist.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
Loading required package: sp

Attaching package: 'sp'

The following object is masked from 'package:unmarked':

    coordinates


Attaching package: 'raster'

The following objects are masked from 'package:unmarked':

    getData, projection

Warning: 22 sites have been discarded because of missing data.
--- finished re-building 'spp-dist.Rnw'

--- re-building 'unmarked.Rnw' using Sweave
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Loading required package: reshape2
Warning in truncateToBinary(y) :
  Some observations were > 1.  These were truncated to 1.
Warning in truncateToBinary(y) :
  Some observations were > 1.  These were truncated to 1.
Warning in truncateToBinary(y) :
  Some observations were > 1.  These were truncated to 1.
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
Warning in rbinom(M * J, 1, prob = p) : NAs produced
--- finished re-building 'unmarked.Rnw'

SUMMARY: processing the following file failed:
  'colext.Rnw'

Error: Vignette re-building failed.
Execution halted